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RNAxplorer − manual page for RNAxplorer 0.9.0


RNAxplorer [OPTION]...


RNAxplorer 0.9.0

The RNAxplorer is a multitool, that offers different sampling and clustering methods to explore RNA energy landscapes.

The RNAxplorer is a multitool, that offers different methods to explore RNA energy landscapes. In default mode (or with −M RSH option) it takes an RNA sequence as input (either stdin or −−sequence parameter) and outputs sampled secondary RNA structures. The repellant sampling heuristic iteratively penalizes base pairs of local minima of structures that have been seen too often. This results in a diverse sample set with the most important low free energy structures.

Another important sampling method (−M RS option) is based on reference

structures (−−struc1 and −−struc2). This method produces structures in the vicinity of these two reference structures. Arbitrary many references can be added if a fasta file is used as input (via stdin).

Often the output of sampling methods has to be coarse grained by local minima

that are defined by a gradient walk. A parallelized gradient descent procedure can be used to retrieve local minima (−M RL option) of sampled structures (input via stdin).
, −−help

Print help and exit


Print help, including all details and hidden options, and exit


Print help, including hidden options, and exit

−V, −−version

Print version and exit

General Options:

Below are command line options which alter the general behavior of this program

−v, −−verbose

Be verbose (default=off)

Repulsive Sampling Options:

Input sequence (default=‘’)


Penalize structures instead of base pairs of local minima, that occure too often. (default=off)


Input structure 1 (default=‘’)


Input structure 2 (default=‘’)


Granularity, i.e. number of samples after which distortion checks are performed (default=‘100’)

−n, −−num−samples=INT

Number of samples in total. The number of samples per iteration is n/g. (default=‘100000’)

−f, −−exploration−factor=FLOAT

Exploration factor (default=‘1’)


Minimum exploration percentage before adding

new repelled structures



Cluster resulting local minima to reduce effective size (default=off)


Output filename for local minima (default=‘’)


Output filename for pseudo−2D file (default=‘’)


Do sampling with non−redundant pbacktrack (default=off)


Input filename for nonredundant samples (default=‘’)

−2, −−explore−two−neighborhood

Explore 2−Neighborhood of local minima, i.e.

eliminate shallow minima



Post processing Filter local minima according to 2−Neighborhood, i.e. eliminate shallow minima (default=off)


Use energy difference instead of kT for penalty (default=off)


proportion factor used to decide whether sampling round was sufficient (default=‘0.1’)


Select additional algorithms which should be included in the calculations. Default is the repellant sampling heuristic. Display more options with −−detailed−help.

−M, −−method=<method>

Set the method used to obtain meshpoint structures for the bisection algorithm


Available options are:


Gradient Walk (default)


Monte Carlo walk


Monte Carlo Walk

with simulated Annealing


Distance based MFE structure



Transition rate computation


Stochastic sampling method with 2D mapping (activate distortion

with −e"N").


Repellant or Attraction sampling


Repellant sampling heuristic


Retrieve local minima. Standard input should be a sequence and a

set of secondary structures (one per line). \


Set the scaling of the Boltzmann factors (default=‘1.’)

The argument provided with this option enables to scale the thermodynamic temperature used in the Boltzmann factors independently from the temperature used to scale the individual energy contributions of the loop types. The Boltzmann factors then become exp(−dG/(kT*betaScale)) where k is the Boltzmann constant, dG the free energy contribution of the state and T the absolute temperature.

−e, −−extended_opt=STRING

Some extended options: N normal distortion (no shift) B alter both potentials at once R relax potential instead of increasing it S shift potential to other structure F shift to first structure V verbose


−i, −−iterations=INT

Set the number of iterations/simulations


−m, −−maxKeep=INT

maxKeep for direct path search


−s, −−maxStore=INT

amount of best solutions to hold per iteration


−r, −−remember=INT

Set the number of structure states to remember in a TABU list


−c, −−circ

Assume a circular (instead of linear) RNA molecule.



Cooling factor used for simulated annealing



start temperature in deg. Celcius



stop temperature in deg. Celcius



Add a penalty for backward moves, i.e. moves along states already visited



just perform a gradient walk starting from a given structure


−D, −−maxD=INT

Maximum base pair distance between meshpoints and references



Maximum base pair distance between meshpoints and reference structure 1



Maximum base pair distance between meshpoints and reference structure 2


Model Details‘:
, −−temp=DOUBLE

Rescale energy parameters to a temperature of temp C. Default is 37C.


Set the percentage of the references distortion value <int> to <double> Can be given for all reference indices (NOTE: the value <double> should be between 0 and 1) (example: "−−p0 2=0.5" − distortion value of sequence 2 will be multiplied with 0.5 before sampling.)

Gradient walker options‘:

Use shift moves for gradient walks.


−P, −−parameter_file=STRING

Use the given parameter file for gradient walks.